Well you also have to take into account the world in which the game is set. Chrono Trigger is based on time travel, so even though Lavos destroyed the "future", you had a way to change it, which made his exploits less damaging. There was always a chance to change it. But with Sephiroth in the FF world, there was no time travel. You went each day knowing that you couldn't change the past. There was no going back and saving Aeris, no going back to prevent sephiroth from even coming into existance. Just think if you weren't even given an option to revive Crono.
So to easily put it, picture yourself in both worlds. Would you be more afraid in CT world going up against Lavos or going up against sephiroth in FF world. Me personally, if I wanted to be in the safest world of the two, I would pick CT because of the time travel and knowing that also Lavos was even scheduled to kill me in "my" lifetime. But sephiroth was trying to destroy the world in my life time if I was one of the characters in FF. So to me, he was the ultimate villain of the two. Time travel plays an important role in watering down Lavos power. If you took out time travel, Lavos would most definitely be the ultimate villain.
And how come no one is talking about the Ten Wise men from Star Ocean 2. They wiped out an entire planet with millions of people on them. Did anybody play Star Ocean 2. To me they should be in the top 5 in ultimate villains.